CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.
CONCLUSIONS
CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.


BACKGROUND
http://bio.ifom-ieo-campus.it/galaxy
Cesaroni
Matteo
M
Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano, Italy. matteo.cesaroni@ifom-ieo-campus.it
Cittaro
Davide
D
Brozzi
Alessandro
A
Pelicci
Pier Giuseppe
PG
Luzi
Lucilla
L
D047369:Chromatin Immunoprecipitation / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software; D014158:Transcription, Genetic